All directives are "lost", but this isn't a Sphinx bug. Sphinx internals simply changed when introducing domains, and all language-specific directives and roles (e.g. "function" and "class") are now grouped in what Sphinx calls "domains".

Simply restoring old 0.6.x code isn't the solution. The broken extension must be re-written for Sphinx 1.0. I don't know, what it does, but it seemingly decorates existing directives. In this case, the proper solution is a special "numpy" domain class, which derives from the standard Python domain and extends the directives and functions accordingly. Ask on the mailing list, if you need advice on how to do this.